The cornea is a specialized epithelium, which protects the eye and maintains transparency for normal vision. Diseases of the cornea or its stem cells (limbal stem cells) affects millions of people worldwide and result from a spectrum of etiologies, ranging from genetic defects to infection, inflammation, or trauma. Vision loss often occurs as the result of transformation of the transparent cornea into a skin-like epithelium. Recent work from our labs and others now reveal that this critical transition may be precipitated by the loss of PAX6 expression. Downregulation of PAX6 causes the loss of cornea features and gene expression and the ectopic activation of skin-like epithelium. Conversely, introduction of PAX6 into skin cells induces many cornea-like features. These studies indicate a critical role of PAX6 for maintaining cornea epithelium, but the mechanisms, which determine cornea vs. skin identity, are still unknown. Our hypothesis is that PAX6 contributes to cornea identity through tissue-specific DNA regulatory elements called enhancers. Enhancers are responsible for coordinating tissue-specific gene expression and for the development of specific cell types. Enhancers are also thought to be of considerable medical importance as genetic variation in and epigenetic regulation of enhancers is thought to play a major role in susceptibility to disease. Despite their biological and medical importance, little is known about the enhancers of the cornea and disease. Advances in chromatin biology and high-throughput sequencing provide new, powerful tools to identify tissue-specific enhancers of the cornea and have the potential to expand our knowledge of cornea disease. Here we propose to (1) identify enhancers, which distinguish cornea from skin epithelium via ChIP-seq; (2) determine how tissue-specific enhancers are regulated in the cornea by chromatin analysis and reporter studies in cultured cells, animal model transplants; and (3) determine the role of PAX6 in the regulation of tissue-specific enhancers. To accomplish these goals, an interdisciplinary approach is needed. The combined expertise and resources of two labs (eye, skin) provides an ideal path to identifying cornea- vs. skin-specific regulation and will result in a better understanding of how ectopic skin features become activated in the cornea. This major effort will result in the identification of genome-wide enhancers in the cornea, critical to stem cell biology and translational studies, and the generation of new genetic reagents to study cornea disease.